LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem       ###
### using energy-conserving DPD (eDPD) simulation                    ###
###                                                                  ###
### Created  : Zhen Li (zhen_li@brown.edu)                           ###
###            Division of Applied Mathematics, Brown University.    ###
###                                                                  ###
### mDPD system setup follows Fig.12 in the publication:             ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis.      ###
### "Energy-conserving dissipative particle dynamics with            ###
### temperature-dependent properties". J. Comput. Phys.,             ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003               ###
########################################################################
units                   lj
dimension               3
boundary                p p p
neighbor                0.2 bin
neigh_modify        every 1 delay 0 check yes

atom_style              edpd
comm_modify vel yes

region     edpd     block -10 10 -10 10 -5 5 units box
create_box          1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
  2 by 2 by 1 MPI processor grid
create_atoms        1 random 16000 276438 NULL
Created 16000 atoms
  using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
  create_atoms CPU = 0.001 seconds
mass                1 1.0
set                 atom * edpd/temp 1.0
Setting atom values ...
  16000 settings made for edpd/temp
set                 atom * edpd/cv 1.0E5
Setting atom values ...
  16000 settings made for edpd/cv

pair_style          edpd 1.58 9872598
#pair_coeff          1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff          1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58                         power 10.54 -3.66 3.44 -4.10                         kappa -0.44 -3.21 5.04  0.00

compute             mythermo all temp
thermo              100
thermo_modify       temp mythermo
thermo_modify       flush yes

velocity            all create 1.0 432982 loop local dist gaussian

region upper block -10.0  10.0   0.0 10.0 -5.0 5.0
region lower block -10.0  10.0 -10.0  0.0 -5.0 5.0

fix         mvv     all mvv/edpd 0.5
fix         upper   all edpd/source region upper  0.01
fix         lower   all edpd/source region lower -0.01

timestep            0.01
run                 500

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair edpd command: doi:10.1016/j.jcp.2014.02.003

@Article{ZLi2014_JCP,
 author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.},
 title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},
 journal = {Journal of Computational Physics},
 year =    {2014},
 volume =  {265},
 pages =   {113--127}
}

@Article{ZLi2015_CC,
 author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.},
 title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},
 journal = {Chemical Communications},
 year =    {2015},
 volume =  {51},
 pages =   {11038--11040}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.78
  ghost atom cutoff = 1.78
  binsize = 0.89, bins = 23 23 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair edpd, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.117 | 5.131 | 5.14 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1              48.942039      0              50.441946      199.82261    
       100   1.0027045      43.752877      0              45.256839      196.18262    
       200   1.0019856      43.711184      0              45.214068      195.21873    
       300   1.0010549      43.708051      0              45.209539      196.54529    
       400   1.0072936      43.694617      0              45.205463      196.01853    
       500   0.99454965     43.693217      0              45.184948      194.56851    
Loop time of 12.7478 on 4 procs for 500 steps with 16000 atoms

Performance: 33888.226 tau/day, 39.222 timesteps/s, 627.560 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 10.639     | 10.877     | 11.121     |   5.7 | 85.32
Neigh   | 1.1777     | 1.1975     | 1.2184     |   1.6 |  9.39
Comm    | 0.28879    | 0.554      | 0.81076    |  27.4 |  4.35
Output  | 0.00025981 | 0.00035629 | 0.00051976 |   0.0 |  0.00
Modify  | 0.077592   | 0.078284   | 0.078852   |   0.2 |  0.61
Other   |            | 0.04102    |            |       |  0.32

Nlocal:           4000 ave        4063 max        3941 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:        5986.75 ave        6036 max        5939 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:         187308 ave      192682 max      181708 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 749234
Ave neighs/atom = 46.827125
Neighbor list builds = 182
Dangerous builds = 0
reset_timestep      0

compute     temp    all edpd/temp/atom
compute     ccT     all chunk/atom bin/1d y 0.0 1.0
fix         stat    all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile

run                 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.382 | 5.391 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.99454965     43.693155      0              45.184886      196.69629    
       100   0.98097933     43.671568      0              45.142946      196.18819    
       200   1.0040512      43.659697      0              45.165679      199.5338     
       300   0.99371064     43.648099      0              45.138571      199.01479    
       400   1.0089291      43.642011      0              45.15531       196.26533    
       500   0.99778837     43.62308       0              45.119669      195.60931    
Loop time of 12.8197 on 4 procs for 500 steps with 16000 atoms

Performance: 33698.231 tau/day, 39.003 timesteps/s, 624.041 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 10.325     | 10.755     | 11.152     |  11.5 | 83.89
Neigh   | 1.1476     | 1.1782     | 1.2083     |   2.7 |  9.19
Comm    | 0.30192    | 0.72837    | 1.1882     |  47.4 |  5.68
Output  | 0.00023835 | 0.00025987 | 0.00032262 |   0.0 |  0.00
Modify  | 0.11909    | 0.11927    | 0.11961    |   0.1 |  0.93
Other   |            | 0.03872    |            |       |  0.30

Nlocal:           4000 ave        4123 max        3896 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost:        5978.75 ave        6017 max        5939 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:         187413 ave      197959 max      177994 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 749653
Ave neighs/atom = 46.853313
Neighbor list builds = 182
Dangerous builds = 0
Total wall time: 0:00:25
